Build Octave and numerical dependencies from source in Ubuntu 20.04

build_oct.sh

#!/bin/bash

# project: build_oct
# version: 1.12 (2023-01-01)
# authors: C. Himpe (0000-0003-2194-6754), M. Koehler (0000-0003-2338-9904)
# license: BSD-2-Clause License (opensource.org/licenses/BSD-2-Clause)
# summary: Build Octave and numerical dependencies from source (in Ubuntu 20.04 with GCC >= 10.3).

# requires hardware: either X86-64 with AVX2 or ARM64 with NEON.
# requires software packages: octave libpcre2-dev libreadline-dev libgmp3-dev libmpfr-dev libfreetype6-dev libgl2ps-dev libfontconfig1-dev libglu1-mesa-dev
# add to .bashrc: alias oct='export OMP_NUM_THREADS=5; $HOME/BUILT/bin/octave-cli'

DEST="$HOME/opt/OCTAVE"
NJOBS=5

XJOBS="-j${NJOBS}"

OPTIM="-O3"

case `uname -m | head -c3` in

    x86)
        OPTIM="$OPTIM -m64 -mavx2 -mfma -march=native -mtune=native -mfpmath=sse -malign-data=cacheline -ftree-vectorize -fno-semantic-interposition"
        ;;

    arm)
        OPTIM="$OPTIM -mcpu=native -floop-optimize -falign-loops -falign-labels -falign-functions -falign-jumps" 
        ;;
esac

FLAGS="$OPTIM -fomit-frame-pointer -I$DEST/include -L$DEST/lib -Wl,-rpath=$DEST/lib -pipe"
LINK="-L$DEST/lib -Wl,-rpath=$DEST/lib"
ALLOC="-fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -lmimalloc"
FLEXI="-lflexiblas -L$DEST/lib"

declare -A AMIMALLOC=(    [TAR]="mimalloc.tar.gz"    [LNK]="https://github.com/microsoft/mimalloc/archive/v"              [VER]="1.7.9"  )
declare -A AOPENBLAS=(    [TAR]="openblas.tar.gz"    [LNK]="https://github.com/xianyi/OpenBLAS/archive/v"                 [VER]="0.3.21" )
declare -A AFLEXIBLAS=(   [TAR]="flexiblas.tar.gz"   [LNK]="https://github.com/mpimd-csc/flexiblas/archive/v"             [VER]="3.2.1"  )
declare -A AQRUPDATENG=(  [TAR]="qrupdate.tar.gz"    [LNK]="https://github.com/mpimd-csc/qrupdate-ng/archive/v"           [VER]="1.1.5"  )
declare -A ASUITESPARSE=( [TAR]="suitesparse.tar.gz" [LNK]="https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v" [VER]="5.13.0" )
declare -A AARPACKNG=(    [TAR]="arpack.tar.gz"      [LNK]="https://github.com/opencollab/arpack-ng/archive/"             [VER]="3.8.0"  )
declare -A ASUNDIALS=(    [TAR]="sundials.tar.gz"    [LNK]="https://github.com/LLNL/sundials/archive/v"                   [VER]="6.5.0"  )
declare -A AOCTAVE=(      [TAR]="octave.tar.gz"      [LNK]="https://ftp.gnu.org/gnu/octave/octave-"                       [VER]="7.3.0"  )

# Setup destination

install -d -m 755 "${DEST}"
install -d -m 755 "${DEST}/include"
install -d -m 755 "${DEST}/lib"
install -d -m 755 "${DEST}/share"
install -d -m 755 "${DEST}/man"
install -d -m 755 "${DEST}/bin"
ln -sf "${DEST}/lib" "${DEST}/lib64"
export PATH="${DEST}/bin":${PATH}

## MIMALLOC

wget -nc -O ${AMIMALLOC[TAR]} ${AMIMALLOC[LNK]}${AMIMALLOC[VER]}.tar.gz
tar -xf ${AMIMALLOC[TAR]} && cd $(tar -tf ${AMIMALLOC[TAR]} | grep -m1 /)
mkdir -p build && cd build &&
cmake .. -DCMAKE_INSTALL_PREFIX=$DEST -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS" &&
make $XJOBS &&
make install
cd ..
cd ..

## OPENBLAS

wget -nc -O ${AOPENBLAS[TAR]} ${AOPENBLAS[LNK]}${AOPENBLAS[VER]}.tar.gz
tar -xf ${AOPENBLAS[TAR]} && cd $(tar -tf ${AOPENBLAS[TAR]} | grep -m1 /)
sed -i "s/COMMON_OPT = -O2/COMMON_OPT = -O3/g" Makefile.system
make $XJOBS CFLAGS="$FLAGS $ALLOC -fPIC" CXXFLAGS="$FLAGS $ALLOC -fPIC" FFLAGS="$FLAGS -fPIC" &&
make PREFIX=$DEST install &&
cd ..

## FLEXIBLAS

wget -nc -O ${AFLEXIBLAS[TAR]} ${AFLEXIBLAS[LNK]}${AFLEXIBLAS[VER]}.tar.gz
tar -xf ${AFLEXIBLAS[TAR]} && cd $(tar -tf ${AFLEXIBLAS[TAR]} | grep -m1 /)
mkdir -p build && cd build &&
cmake .. -DCMAKE_C_FLAGS="$FLAGS $ALLOC" -DCMAKE_CXX_FLAGS="$FLAGS $ALLOC" -DCMAKE_Fortran_FLAGS="$FLAGS" -DCMAKE_LD_FLAGS="$LINK" \
         -DCMAKE_INSTALL_PREFIX=$DEST \
         -DEXTRA="OPENBLAS" \
         -DOPENBLAS_LIBRARY="$DEST/lib/libopenblas.so;gfortran;gomp;m"\
         -DFLEXIBLAS_DEFAULT=OPENBLAS &&
make $XJOBS &&
make install &&
cd ..
cd ..

## QRUPDATENG

wget -nc -O ${AQRUPDATENG[TAR]} ${AQRUPDATENG[LNK]}${AQRUPDATENG[VER]}.tar.gz
tar -xf ${AQRUPDATENG[TAR]} && cd $(tar -tf ${AQRUPDATENG[TAR]} | grep -m1 /)
mkdir -p build && cd build &&
cmake .. -DCMAKE_C_FLAGS="$FLAGS $ALLOC" -DCMAKE_CXX_FLAGS="$FLAGS $ALLOC" -DCMAKE_Fortran_FLAGS="$FLAGS" -DCMAKE_LD_FLAGS="$LINK" \
         -DCMAKE_INSTALL_PREFIX=$DEST \
         -DBUILD_SHARED_LIBS=ON \
         -DBLAS_LIBRARIES=$DEST/lib/libflexiblas.so \
         -DLAPACK_LIBRARIES=$DEST/lib/libflexiblas.so &&
make $XJOBS &&
make install &&
cd ..
cd ..

## SUITESPARSE

wget -nc -O ${ASUITESPARSE[TAR]} ${ASUITESPARSE[LNK]}${ASUITESPARSE[VER]}.tar.gz
tar -xf ${ASUITESPARSE[TAR]} && cd $(tar -tf ${ASUITESPARSE[TAR]} | grep -m1 /)
sed -i "s/( cd GraphBLAS/#( cd GraphBLAS/g" Makefile # CHECK ON UPDATE
sed -i "351s/.*/        LDLIBS += -lrt -L\$(INSTALL_LIB)/" SuiteSparse_config/SuiteSparse_config.mk # CHECK ON UPDATE
make JOBS=${NJOBS} $XJOBS library CFLAGS="$FLAGS $ALLOC" CXXFLAGS="$FLAGS $ALLOC" FFLAGS="$FLAGS" LDFLAGS="$LINK" BLAS="$FLEXI" LAPACK="$FLEXI" &&
make install INSTALL=$DEST BLAS="$FLEXI" LAPACK="$FLEXI" CFLAGS="$FLAGS $ALLOC" CXXFLAGS="$FLAGS $ALLOC" FFLAGS="$FLAGS" LDFLAGS="$LINK" &&
cd ..

## SUNDIALS

wget -nc -O ${ASUNDIALS[TAR]} ${ASUNDIALS[LNK]}${ASUNDIALS[VER]}.tar.gz
tar -xf ${ASUNDIALS[TAR]} && cd sundials-${ASUNDIALS[VER]}
mkdir -p build && cd build &&
cmake .. -DCMAKE_INSTALL_PREFIX=$DEST \
         -DCMAKE_C_FLAGS_RELEASE="$FLAGS $ALLOC" \
         -DCMAKE_CXX_FLAGS_RELEASE="$FLAGS $ALLOC" \
         -DCMAKE_Fortran_FLAGS_RELEASE="$FLAGS" \
         -DCMAKE_LD_FLAGS="$LINK" \
         -DCMAKE_BUILD_TYPE=Release -DEXAMPLES_INSTALL_PATH=$DEST/examples \
         -DENABLE_LAPACK=ON -DLAPACK_LIBRARIES=$DEST/lib/libflexiblas.so \
         -DENABLE_KLU=ON -DKLU_INCLUDE_DIR=$DEST/include -DKLU_LIBRARY_DIR=$DEST/lib \
         -DENABLE_OPENMP=ON &&
make $XJOBS &&
make install &&
cd ..
cd ..

## ARPACKNG

wget -nc -O ${AARPACKNG[TAR]} ${AARPACKNG[LNK]}${AARPACKNG[VER]}.tar.gz
tar -xf ${AARPACKNG[TAR]} && cd $(tar -tf ${AARPACKNG[TAR]} | grep -m1 /)
mkdir -p build && cd build &&
cmake .. -DCMAKE_C_FLAGS="$FLAGS $ALLOC" -DCMAKE_CXX_FLAGS="$FLAGS $ALLOC" -DCMAKE_Fortran_FLAGS="$FLAGS" \
         -DCMAKE_INSTALL_PREFIX=$DEST \
         -DBUILD_SHARED_LIBS=ON \
         -DBLAS_LIBRARIES="$FLEXI" \
         -DLAPACK_LIBRARIES="$FLEXI" &&
make $XJOBS &&
make install &&
cd ..
cd ..

## OCTAVE

wget -nc -O ${AOCTAVE[TAR]} ${AOCTAVE[LNK]}${AOCTAVE[VER]}.tar.gz
tar -xf ${AOCTAVE[TAR]} && cd $(tar -tf ${AOCTAVE[TAR]} | grep -m1 /)
./configure CFLAGS="$FLAGS $ALLOC" CXXFLAGS="$FLAGS $ALLOC" FFLAGS="$FLAGS" LDFLAGS="$LINK" --prefix=$DEST \
            --disable-java --disable-gui --without-qt \
            --with-blas="$FLEXI" --with-lapack="$FLEXI" \
            --with-qrupdate-includedir=$DEST/include --with-qrupdate-libdir=$DEST/lib \
            --with-arpack-includedir=$DEST/include --with-arpack-libdir=$DEST/lib \
            --with-klu-includedir=$DEST/include --with-klu-libdir=$DEST/lib \
            --with-sundials_ida-includedir=$DEST/include --with-sundials_ida-libdir=$DEST/lib \
            --with-sundials_nvecserial-includedir=$DEST/include --with-sundials_nvecserial-libdir=$DEST/lib \
            --with-sundials_sunlinsolklu-includedir=$DEST/include --with-sundials_sunlinsolklu-libdir=$DEST/lib \
            --with-umfpack-includedir=$DEST/include --with-umfpack-libdir=$DEST/lib \
            --with-cxsparse-includedir=$DEST/include --with-cxsparse-libdir=$DEST/lib \
            --with-cholmod-includedir=$DEST/include --with-cholmod-libdir=$DEST/lib \
            --with-ccolamd-includedir=$DEST/include --with-ccolamd-libdir=$DEST/lib \
            --with-colamd-includedir=$DEST/include --with-colamd-libdir=$DEST/lib \
            --with-camd-includedir=$DEST/include --with-camd-libdir=$DEST/lib \
            --with-amd-includedir=$DEST/include --with-amd-libdir=$DEST/lib \
            --with-suitesparseconfig-includedir=$DEST/include --with-suitesparseconfig-libdir=$DEST/lib &&
make $XJOBS &&
make install PREFIX=$DEST
cd ..

exit 0

This is great! One minor problem though. It appears that it octave doesn't integrate with sundials.

octave:1> [t,y] = ode15s(@(t,y) -10*t, [0, 2], 1);
error: __ode15__: support for sundials_ida, sundials_nvecserial was unavailable or disabled when Octave was built
error: called from
    ode15s at line 315 column 22

Any thoughts?

This is odd. Can you attach the config.log in the octave folder? Thanks.

I've created a gist of the config.log.

This bit seems relevant.

78722 configure:75567: $PKG_CONFIG --exists --print-errors "sundials_nvecserial"
78723 Package sundials_nvecserial was not found in the pkg-config search path.
78724 Perhaps you should add the directory containing `sundials_nvecserial.pc'
78725 to the PKG_CONFIG_PATH environment variable
78726 No package 'sundials_nvecserial' found

Sorry, I cannot reproduce this on my system. Could you check if the sundials package was successfully built?

You're right. flexiblas-3.0.4 builds and make test passes, but

~/BUILT/SuiteSparse-5.10.1/sundials-5.8.0/build $ cmake ..
-- SUNDIALS_GIT_VERSION: 
-- Using int64_t for indices
-- Determining Fortran name-mangling scheme... OK
Appending C RELEASE flags
Appending Fortran RELEASE flags
-- Looking for LAPACK libraries... OK
-- LAPACK_LIBRARIES:  /home/jwscook/BUILT/lib/libflexiblas.so
-- Skipped LAPACK tests, assuming LAPACK works with SUNDIALS. Set LAPACK_WORKS=FALSE to (re)run compatibility test.
CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
  Could NOT find KLU (missing: KLU_LIBRARY KLU_LIBRARIES)
Call Stack (most recent call first):
  /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
  cmake/tpl/FindKLU.cmake:94 (find_package_handle_standard_args)
  cmake/tpl/SundialsKLU.cmake:48 (find_package)
  cmake/SundialsSetupTPLs.cmake:103 (include)
  CMakeLists.txt:168 (include)


-- Configuring incomplete, errors occurred!

That's all I've got time for until Monday, I'm afraid.

Alright.
The first thing that strikes me as odd is the path ~/BUILT/SuiteSparse-5.10.1/sundials-5.8.0/build $. I suggest to make a fresh folder, place the build_oct.sh inside and re-run it; Sundials should not have been built below SuiteSparse. I assume SuiteSparse already failed to built?

Either installing libpcre3-dev or starting again from a new directory as suggest worked. Thanks again :)